Fanwei Kong

Fanwei Kong, Shawn Shadden

Patient-specific cardiac modeling combines geometries of the heart derived from medical images and biophysical simulations to predict various aspects of cardiac function. However, generating simulation-suitable models of the heart from patient image data often requires complicated procedures and significant human effort. We present a fast and automated deep-learning method to construct simulation-suitable models of the heart from medical images. The approach constructs meshes from 3D patient images by learning to deform a small set of deformation handles on a whole heart template. For both 3D CT and MR data, this method achieves promising accuracy for whole heart reconstruction, consistently outperforming prior methods in constructing simulation-suitable meshes of the heart. When evaluated on time-series CT data, this method produced more anatomically and temporally consistent geometries than prior methods, and was able to produce geometries that better satisfy modeling requirements for cardiac flow simulations. Our source code and pretrained networks are available at https://github.com/fkong7/HeartDeformNets.

Arjun Narayanan, Fanwei Kong, Shawn Shadden

We present a deep learning model to automatically generate computer models of the human heart from patient imaging data with an emphasis on its capability to generate thin-walled cardiac structures. Our method works by deforming a template mesh to fit the cardiac structures to the given image. Compared with prior deep learning methods that adopted this approach, our framework is designed to minimize mesh self-penetration, which typically arises when deforming surface meshes separated by small distances. We achieve this by using a two-stage diffeomorphic deformation process along with a novel loss function derived from the kinematics of motion that penalizes surface contact and interpenetration. Our model demonstrates comparable accuracy with state-of-the-art methods while additionally producing meshes free of self-intersections. The resultant meshes are readily usable in physics based simulation, minimizing the need for post-processing and cleanup.

Fanwei Kong, Sascha Stocker, Perry S. Choi et al.

Congenital heart disease (CHD) encompasses a spectrum of cardiovascular structural abnormalities, often requiring customized treatment plans for individual patients. Computational modeling and analysis of these unique cardiac anatomies can improve diagnosis and treatment planning and may ultimately lead to improved outcomes. Deep learning (DL) methods have demonstrated the potential to enable efficient treatment planning by automating cardiac segmentation and mesh construction for patients with normal cardiac anatomies. However, CHDs are often rare, making it challenging to acquire sufficiently large patient cohorts for training such DL models. Generative modeling of cardiac anatomies has the potential to fill this gap via the generation of virtual cohorts; however, prior approaches were largely designed for normal anatomies and cannot readily capture the significant topological variations seen in CHD patients. Therefore, we propose a type- and shape-disentangled generative approach suitable to capture the wide spectrum of cardiac anatomies observed in different CHD types and synthesize differently shaped cardiac anatomies that preserve the unique topology for specific CHD types. Our DL approach represents generic whole heart anatomies with CHD type-specific abnormalities implicitly using signed distance fields (SDF) based on CHD type diagnosis, which conveniently captures divergent anatomical variations across different types and represents meaningful intermediate CHD states. To capture the shape-specific variations, we then learn invertible deformations to morph the learned CHD type-specific anatomies and reconstruct patient-specific shapes. Our approach has the potential to augment the image-segmentation pairs for rarer CHD types for cardiac segmentation and generate cohorts of CHD cardiac meshes for computational simulation.

Elena Martinez, Beatrice Moscoloni, Matteo Salvador et al.

Combining physics-based modeling with data-driven methods is critical to enabling the translation of computational methods to clinical use in cardiology. The use of rigorous differential equations combined with machine learning tools allows for model personalization with uncertainty quantification in time frames compatible with clinical practice. However, accurate and efficient surrogate models of cardiac function, built from physics-based numerical simulation, are still mostly geometry-specific and require retraining for different patients and pathological conditions. We propose a novel computational pipeline to embed cardiac anatomies into full-field surrogate models. We generate a dataset of electrophysiology simulations using a complex multi-scale mathematical model coupling partial and ordinary differential equations. We adopt Branched Latent Neural Maps (BLNMs) as an effective scientific machine learning method to encode activation maps extracted from physics-based numerical simulations into a neural network. Leveraging large deformation diffeomorphic metric mappings, we build a biventricular anatomical atlas and parametrize the anatomical variability of a small and challenging cohort of 13 pediatric patients affected by Tetralogy of Fallot. We propose a novel statistical shape modeling based z-score sampling approach to generate a new synthetic cohort of 52 biventricular geometries that are compatible with the original geometrical variability. This synthetic cohort acts as the training set for BLNMs. Our surrogate model demonstrates robustness and great generalization across the complex original patient cohort, achieving an average adimensional mean squared error of 0.0034. The Python implementation of our BLNM model is publicly available under MIT License at https://github.com/StanfordCBCL/BLNM.

Fanwei Kong, Nathan Wilson, Shawn C. Shadden

Automated construction of surface geometries of cardiac structures from volumetric medical images is important for a number of clinical applications. While deep-learning-based approaches have demonstrated promising reconstruction precision, these approaches have mostly focused on voxel-wise segmentation followed by surface reconstruction and post-processing techniques. However, such approaches suffer from a number of limitations including disconnected regions or incorrect surface topology due to erroneous segmentation and stair-case artifacts due to limited segmentation resolution. We propose a novel deep-learning-based approach that directly predicts whole heart surface meshes from volumetric CT and MR image data. Our approach leverages a graph convolutional neural network to predict deformation on mesh vertices from a pre-defined mesh template to reconstruct multiple anatomical structures in a 3D image volume. Our method demonstrated promising performance of generating whole heart reconstructions with as good or better accuracy than prior deep-learning-based methods on both CT and MR data. Furthermore, by deforming a template mesh, our method can generate whole heart geometries with better anatomical consistency and produce high-resolution geometries from lower resolution input image data. Our method was also able to produce temporally consistent surface mesh predictions for heart motion from CT or MR cine sequences, and therefore can potentially be applied for efficiently constructing 4D whole heart dynamics. Our code and pre-trained networks are available at https://github.com/fkong7/MeshDeformNet

Fanwei Kong, Aaron Brown, Michael Loecher et al.

Intracardiac flow patterns are shaped by the coupled motion of the cardiac chambers and heart valves and provide important information about cardiac function. However, clinical flow imaging remains limited by exam times, noise, resolution, and incomplete details of the three-dimensional flow. Computational fluid dynamics (CFD) can potentially provide detailed flow quantification and predictive insight into treatment outcomes, but clinical translation requires frameworks that reproduce patient-specific measurements while balancing physiological realism, computational cost, and modeling effort. Herein, we present an image-based, patient-specific computational framework for simulating whole-heart intracardiac hemodynamics that balances physiological fidelity with computational efficiency. The framework first employs machine learning-based segmentation and mesh propagation to reconstruct moving cardiac anatomies from time-resolved images. CFD simulations are then performed to resolve blood flow in deforming domains, while resistive immersed surfaces (RIS) are used to model all four cardiac valves with physiologically realistic opening and closing dynamics. The framework was applied to model hemodynamics in a healthy adult and a pediatric patient with complex congenital heart disease (CHD). In the healthy case, the simulations reproduced physiologic pressure-volume behavior, valve timing, and ventricular vortex formation. In the CHD case, simulated chamber and vessel pressures showed agreement with cardiac catheterization measurements. Simulated flow fields were qualitatively consistent with 4D-Flow MRI, while providing higher-resolution visualization of flow structures that were partially obscured by imaging artifacts. Comparison between the healthy and CHD cases further revealed altered diastolic flow organization and elevated normalized viscous dissipation in the CHD heart.

Riccardo Tenderini, Luca Pegolotti, Fanwei Kong et al.

This work introduces AD-SVFD, a deep learning model for the deformable registration of vascular shapes to a pre-defined reference and for the generation of synthetic anatomies. AD-SVFD operates by representing each geometry as a weighted point cloud and models ambient space deformations as solutions at unit time of ODEs, whose time-independent right-hand sides are expressed through artificial neural networks. The model parameters are optimized by minimizing the Chamfer Distance between the deformed and reference point clouds, while backward integration of the ODE defines the inverse transformation. A distinctive feature of AD-SVFD is its auto-decoder structure, that enables generalization across shape cohorts and favors efficient weight sharing. In particular, each anatomy is associated with a low-dimensional code that acts as a self-conditioning field and that is jointly optimized with the network parameters during training. At inference, only the latent codes are fine-tuned, substantially reducing computational overheads. Furthermore, the use of implicit shape representations enables generative applications: new anatomies can be synthesized by suitably sampling from the latent space and applying the corresponding inverse transformations to the reference geometry. Numerical experiments, conducted on healthy aortic anatomies, showcase the high-quality results of AD-SVFD, which yields extremely accurate approximations at competitive computational costs.